PROSITE documentation PDOC00517

Chromo domain signature and profile

The 'chromo' (CHRromatin Organization MOdifier) domain [1,2,3,4] is a conserved region of about 60 amino acids which was first identified in the drosophila chromatin proteins HP1 and Polycomb. Chromo domain have now been found in single or multiple copies in a variety of eukaryotic proteins with diverse structures and activities, most or all of which are connected with chromosome structure/function. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro [5].

HP1 was found to have a second chromo domain in the C-terminal half of the protein, called the 'chromo shadow' domain, with weak but significant sequence similarity to the N-terminal chromo domain. Various chromo shadow domains have been shown to mediate self-association, pointing to a general property of this motif. However, chromo shadow domains have been implicated in a variety of heterologous interactions as well. Hence the chromo shadow domain of human HP1-family proteins has been found to bind to lamin B receptor in yeast two hybrid protein assay [5].

The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three β strands packed against an α helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [5].

Some proteins known to contain a chromo or chromo shadow domain are listed below:

• Drosophila heterochromatin protein Su(var)205 (HP1).
• Human heterochromatin protein HP1 α.
• Mammalian modifier 1 and modifier 2.
• Fission yeast swi6, a protein involved in the repression of the silent mating-type loci mat2 and mat3.
• Drosophila protein Polycomb (Pc).
• Mammalian modifier 3, a homolog of Pc.
• Drosophila protein Su(var)3-9, a suppressor of position-effect variegation.
• Human Mi-2 autoantigen, characterisitic of dermatomyosis.
• Fungal retrotranposon polyproteins: 'skippy' from Fusarium oxysporum, 'grasshopper' and 'MAGGY' from Magnaporthe grisea and CfT-1 from Cladosporium fulvum.
• Fission yeast hypothetical protein SpAC18G6.02c.
• Caenorhabditis elegans hypothetical protein C29H12.5
• Caenorhabditis elegans hypothetical protein ZK1236.2.
• Caenorhabditis elegans hypothetical protein T09A5.8.
• Mammalian DNA-binding/helicase proteins CHD-1 to CHD-4.
• Yeast protein CHD1.
• Drosophila male-specific lethal-3 protein (MSL-3).
• Drosophila males absent on the first (MOF).
• Tetrahymena thermophila Pdds (programmed DNA degradation), factors that appear to participate in the recognition and removal of DNA during macronuclear differentiation.

The signature pattern for this domain corresponds to its best conserved section, which is located in its central part. We also developed a profile, which covers the entire chromo and chromo shadow domains.